[2024-01-24 11:05:25,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference
[2024-01-24 11:05:26,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,863] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d03215-cf61-4ea0-97a1-53ea172b5202/GCF_003651245.1_ASM365124v1_genomic.fna.gz | prodigal -d GCF_003651245.1_ASM365124v1_genomic.fna/cds.fna -a GCF_003651245.1_ASM365124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:38,600] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:38,601] [INFO] Task started: HMMsearch
[2024-01-24 11:05:38,601] [INFO] Running command: hmmsearch --tblout GCF_003651245.1_ASM365124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/reference_markers.hmm GCF_003651245.1_ASM365124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:38,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:38,869] [INFO] Found 6/6 markers.
[2024-01-24 11:05:38,904] [INFO] Query marker FASTA was written to GCF_003651245.1_ASM365124v1_genomic.fna/markers.fasta
[2024-01-24 11:05:38,905] [INFO] Task started: Blastn
[2024-01-24 11:05:38,905] [INFO] Running command: blastn -query GCF_003651245.1_ASM365124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/reference_markers.fasta -out GCF_003651245.1_ASM365124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:40,004] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:40,009] [INFO] Selected 28 target genomes.
[2024-01-24 11:05:40,009] [INFO] Target genome list was writen to GCF_003651245.1_ASM365124v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:40,024] [INFO] Task started: fastANI
[2024-01-24 11:05:40,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d03215-cf61-4ea0-97a1-53ea172b5202/GCF_003651245.1_ASM365124v1_genomic.fna.gz --refList GCF_003651245.1_ASM365124v1_genomic.fna/target_genomes.txt --output GCF_003651245.1_ASM365124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:01,904] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:01,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:01,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:01,925] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:01,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:01,925] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	80.5393	671	1344	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	79.7417	561	1344	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.7222	566	1344	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.6187	574	1344	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	79.3717	519	1344	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.3593	545	1344	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	79.3419	549	1344	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.3262	560	1344	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.3074	645	1344	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	79.2988	538	1344	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.2591	588	1344	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	79.251	539	1344	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	79.2197	645	1344	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.2033	540	1344	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	79.1921	659	1344	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.0645	487	1344	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.0514	539	1344	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7055	413	1344	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.6075	526	1344	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5878	449	1344	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.5358	512	1344	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.508	447	1344	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.4076	376	1344	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.4074	458	1344	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2957	415	1344	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.2163	410	1344	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.1145	433	1344	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1113	430	1344	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:01,927] [INFO] DFAST Taxonomy check result was written to GCF_003651245.1_ASM365124v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:01,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:01,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:01,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/checkm_data
[2024-01-24 11:06:01,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:01,970] [INFO] Task started: CheckM
[2024-01-24 11:06:01,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003651245.1_ASM365124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003651245.1_ASM365124v1_genomic.fna/checkm_input GCF_003651245.1_ASM365124v1_genomic.fna/checkm_result
[2024-01-24 11:06:40,620] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:40,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:40,644] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:40,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:40,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003651245.1_ASM365124v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:40,645] [INFO] Task started: Blastn
[2024-01-24 11:06:40,645] [INFO] Running command: blastn -query GCF_003651245.1_ASM365124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c248c1c-4140-42b5-bc94-06dfd49f7a9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003651245.1_ASM365124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:42,823] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:42,828] [INFO] Selected 22 target genomes.
[2024-01-24 11:06:42,828] [INFO] Target genome list was writen to GCF_003651245.1_ASM365124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:42,845] [INFO] Task started: fastANI
[2024-01-24 11:06:42,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d03215-cf61-4ea0-97a1-53ea172b5202/GCF_003651245.1_ASM365124v1_genomic.fna.gz --refList GCF_003651245.1_ASM365124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003651245.1_ASM365124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:00,230] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:00,252] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:00,253] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003651245.1	s__Roseovarius spongiae	100.0	1343	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003072125.1	s__Roseovarius sediminicola	80.5159	673	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	79.8547	409	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCF_002925845.1	s__Roseovarius nitratireducens	79.7411	560	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCF_900156535.1	s__Roseovarius nanhaiticus	79.6896	595	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014359765.1	s__Roseovarius sp014359765	79.6211	486	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	79.582	478	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.4055	565	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	79.3695	599	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900109855.1	s__Roseovarius tolerans	79.3622	520	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_003316635.1	s__Roseovarius dicentrarchi	79.3423	549	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	79.3222	644	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_900109035.1	s__Cribrihabitans marinus	79.306	563	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900142665.1	s__Roseovarius pacificus	79.2421	541	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_000152625.1	s__Roseovarius nubinhibens	79.2405	587	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_002917925.1	s__Roseovarius confluentis	79.1555	556	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_003385555.1	s__Rhodosalinus sediminis	78.9903	481	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.5445	443	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	78.446	375	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.4453	441	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	78.4094	461	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.399	459	1344	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:00,254] [INFO] GTDB search result was written to GCF_003651245.1_ASM365124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:00,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:00,262] [INFO] DFAST_QC result json was written to GCF_003651245.1_ASM365124v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:00,262] [INFO] DFAST_QC completed!
[2024-01-24 11:07:00,263] [INFO] Total running time: 0h1m35s